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I charged my normal development rate for the initial work.
Then duplicated/edited the site and charged it as maintenance.
I don't see it as any different from developing a site and then adding functionality/maintaining/optimising, etc.
I don't like all this licensing lark, I think it just annoys clients.
This kind of stepwise pricing can be worth it if developing a single site may be too expensive for one customer, but when you know or reasonably can assume that others will also buy it, is worth the effort. With my project, every customer including the first one knew about the price discount and that the project could be distributed to others. Your situation is different because you already did the development for one organization. You should carefully read the contract you have with them to see if you are allowed to resell the same site twice; it could well be so that the first organization owns rights which prohibit reselling.